MolNFT v1 · #55534 · protein
Plasmodium vivax N-myristoyltransferase in complex with YNC12-CoA thioester.
2YNC · Glycylpeptide N-tetradecanoyltransferase: “Plasmodium vivax N-myristoyltransferase in complex with YNC12-CoA thioester.”. X-ray diffraction, 4 ligands (YNC, MG, CL), 11 pockets (best druggability 0.83). MolNFT v1 #55534 on…
- PDB
- 2YNC
- Type
- protein
- Length
- 1,138 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycylpeptide N-tetradecanoyltransferase
- EC
- 2.3.1.97
- UniProt
- A5K1A2
- Ligands
- YNC, MG, CL, SO4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 384 | 28% helix, 29% strand | A5K1A2 |
| C | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 370 | 26% helix, 31% strand | A5K1A2 |
Ligands and binding sites
- YNC · Tetradec-13-ynoic acid - coa thioester · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 5 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains A, B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.83 | 0.85 | 92 | empty |
| 2 | 897 | 0.78 | 0.81 | 85 | YNC, MG |
| 3 | 880 | 0.78 | 0.81 | 74 | YNC, MG |
| 4 | 865 | 0.77 | 0.80 | 81 | YNC, MG |
| 5 | 73 | 0.51 | 0.85 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 586 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 249 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2YNC · Plasmodium vivax N-myristoyltransferase in complex with YnC12-CoA thioester. · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A5K1A2
- Elsewhere: RCSB PDB 2YNC · PDBe 2YNC · UniProt A5K1A2
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